Induced pluripotent stem (iPS) cells have a tremendous potential for aidvancing our understanding of human development and disease. To help unlock this potential we have organized a program to (A) comprehensively identify the genetic and epigenetic components of the regulatory network that maintains cells in a pluripotent state;(B) characterize culture-induced variation in the activites of these components in pluripotent cells;and (C) characterize temporal variation in their activities during induction of pluripotency with defined factors. To achieve these goals, we have formulated four interdependent projects: Project I (Meissner) will (1) characterize transcriptional coregulators and small non-coding RNAs that modulate the activity of the core pluripotency transcription factors, and (2) define and isolate subpopulations from pluripotent cell cultures to characterize their transcriptional and epigenetic states. Project II (Rinn) will characterize long non-coding RNAs expressed in pluripotent cells and elucidate their role in remodeling the epigenetic landscape during reprogramming. Project III (Mikkelsen) will characterize the cis-regulatory modules that direct activation, maintenace and repression of gene expression in pluripotent cells by recruiting transcription factors and their coregulators to key genomic loci. Project IV (Eggan) will characterize the inheritance patterns and maintenance of inactivated X chromosomes during reprogramming and in pluripotent cell cultures. The four projects rely on complementary use of innovative high-throughput genomic and proteomic technologies to profile high-quality iPS cell lines. The integration of data and insights from each of the projects will generate a comprehensive view of protein-protein, protein-RNA and protein-DNA interactions essential to the maintenace of pluripotency (goal A). This intergrated view will then guide studies of culture- induced and temporal variation in the network (goals B and C).

Public Health Relevance

Induced pluripotent stem cells are a potential revolutionary tool for disease modeling, drug screening and regenerative medicine. This program is organized to fully characterize the molecular properties of these cells, which is essential to ensure that their use in biomedicine is effective and safe.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Program Projects (P01)
Project #
5P01GM099117-04
Application #
8717677
Study Section
Special Emphasis Panel (ZGM1-GDB-8 (IP))
Program Officer
Haynes, Susan R
Project Start
2011-08-01
Project End
2016-07-31
Budget Start
2014-08-01
Budget End
2015-07-31
Support Year
4
Fiscal Year
2014
Total Cost
$2,102,947
Indirect Cost
$579,557
Name
Harvard University
Department
Anatomy/Cell Biology
Type
Schools of Arts and Sciences
DUNS #
082359691
City
Cambridge
State
MA
Country
United States
Zip Code
02138
Choi, Jiho; Clement, Kendell; Huebner, Aaron J et al. (2017) DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells. Cell Stem Cell 20:706-719.e7
Merkle, Florian T; Ghosh, Sulagna; Kamitaki, Nolan et al. (2017) Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations. Nature 545:229-233
Smith, Zachary D; Shi, Jiantao; Gu, Hongcang et al. (2017) Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer. Nature 549:543-547
Melé, Marta; Mattioli, Kaia; Mallard, William et al. (2017) Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs. Genome Res 27:27-37
Lin, Shuibin; Choe, Junho; Du, Peng et al. (2016) The m(6)A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells. Mol Cell 62:335-345
Groff, Abigail F; Sanchez-Gomez, Diana B; Soruco, Marcela M L et al. (2016) In Vivo Characterization of Linc-p21 Reveals Functional cis-Regulatory DNA Elements. Cell Rep 16:2178-2186
Santos, David P; Kiskinis, Evangelos; Eggan, Kevin et al. (2016) Comprehensive Protocols for CRISPR/Cas9-based Gene Editing in Human Pluripotent Stem Cells. Curr Protoc Stem Cell Biol 38:5B.6.1-5B.6.60
Hacisuleyman, Ezgi; Shukla, Chinmay J; Weiner, Catherine L et al. (2016) Function and evolution of local repeats in the Firre locus. Nat Commun 7:11021
Liu, Lin L; Brumbaugh, Justin; Bar-Nur, Ori et al. (2016) Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells. Cell Rep 17:3395-3406
Tsankov, Alexander M; Akopian, Veronika; Pop, Ramona et al. (2015) A qPCR ScoreCard quantifies the differentiation potential of human pluripotent stem cells. Nat Biotechnol 33:1182-92

Showing the most recent 10 out of 55 publications